Profiling Enzyme Activities In Vivo Using Click Chemistry Methods Anna E Speers, Benjamin F Cravatt  Chemistry & Biology  Volume 11, Issue 4, Pages 535-546 (April 2004) DOI: 10.1016/j.chembiol.2004.03.012

Figure 1 Comparison of Standard and Click Chemistry ABPP ABPP probes consist of a reactive group (RG), binding group (BG), and tag (e.g., rhodamine and/or biotin). In contrast to standard ABPP, click chemistry ABPP allows for the profiling of living cells and organisms by treating these specimens with tag-free azide- or alkyne-modified probes, which are then conjugated in vitro to the complementary alkyne- or azide-modified tag under cycloaddition reaction conditions to visualize probe-labeled proteins. Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 2 Chemical Structures of Azide and Alkyne Probes and Tags Note: TriN3, 7 was synthesized on solid phase and thus has an amide group in the X position where it was attached to the resin. Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 3 Comparison of In Vitro Labeling of Enzymes in Complex Proteomes Using PSN3/Rh≡ and PS9≡/RhN3 CC Pairs (A) Three target enzymes, ALDH-1, ECH-1, and GSTω, are labeled by both CC pairs; Rh≡ gives rise to significant background in the presence and absence of PSN3. Δ, heat-denatured proteomes. (B) Dependence of protein labeling on click chemistry reaction components. Strongest fluorescent signals are observed when CuSO4, ligand, and TCEP are used in the cycloaddition reaction. (C and D) Fluorescence intensity of GSTω labeling (in homogenates of MDA-MB-435 cells) as a function of (C) tag concentration and (D) cycloaddition reaction time. A tag concentration of 50 μM is sufficient to achieve maximum fluorescent intensity in 1 hr (C). The PSN3/Rh≡ CC pair reacts to completion approximately four times faster than the PS9≡/RhN3 CC pair (D; 50 μM tag). Note: for (A) and (B) (and subsequent figures), fluorescent gel images are shown in gray scale. Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 4 In Vivo Labeling of ALDH-1 in Mouse Liver (A) Comparison of CC pairs. Clear fluorescent signals are observed for ALDH-1 when mice are treated (10, 20 mg/kg i.p.) with PS9≡ but not PSN3. In vitro-labeled ALDH-1 shown for comparison (lanes 2 and 9) along with the associated heat controls (Δ, lanes 1 and 10). (B) In vitro chemical inhibition of ALDH-1 by disulfiram (0–100 μM added 1 hr prior to reaction with 5 μM PS9≡). (C) In vivo chemical inhibition of ALDH-1 by disulfiram results in a 2.6-fold reduction in labeling intensity. Representative gel image shown above the bar graph (n = 3 per group). Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 5 Time and Concentration Dependence of In Situ Probe Labeling of T-47D Cancer Cells In situ protein labeling as a function of probe incubation time ([A] and [B], 15 min to 4 hr, 25 μM probe) and concentration ([C] and [D], 5–100 μM probe, 1 hr). Graphical representation of protein labeling intensities (each normalized to percent of maximum intensity) for time and concentration dependence gels shown in (B) and (D), respectively. For graph of absolute labeling intensities, see Supplemental Figure S2 on Chemistry & Biology's website. Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 6 Comparison of In Situ and In Vitro Enzyme Activity Profiles of T-47D and MDA-MB-231 Cancer Cell Lines (A) While some enzyme activities are labeled with equal intensity in situ and in vitro (e.g., GSTω), other enzyme activities show significantly more probe labeling in situ compared to in vitro (e.g., VLCAD). Notable differences in protein activity between the invasive (MDA-MB-231) and noninvasive (T-47D) cell lines were also observed (e.g., ECH-2). Δ, heat-denatured proteomes. (B and C) Levels of representative enzyme activities compared (B) in situ versus in vitro (shown for PSN3/Rh≡) and (C) in situ-labeled T-47D versus MDA-MB-231 cells (n = 3 per group). Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)

Figure 7 Q-Sepharose Chromatography of In Situ and In Vitro Probe-Labeled T-47D Proteomes Enhances the Visualization of Differentially Expressed Enzyme Activities (A) Several proteins that exhibited stronger or exclusive labeling in situ are boxed, including enzyme activities that could be detected by 1D-SDS-PAGE analysis of whole proteomes (e.g., ECH-2, PDI, VLCAD; see Figure 6A) and other proteins that were more effectively visualized following Q fractionation (asterisks). (B) MS peptide data (black text) for a novel human enoyl-CoA hydratase variant, ECH-2. Residues that distinguish ECH-2 from the previously identified ECH-1 [39] are boxed. Chemistry & Biology 2004 11, 535-546DOI: (10.1016/j.chembiol.2004.03.012)